Megaman Legends: System's War
by lunateix
Summary: Megaman managed to deactivate the Mother System, things should get easier now, right? Well unfortunately he's awakened the greatest threat from his past and it threatens to destroy everything he's worked so hard to protect.
1. Chapter 1

Some Author's Notes: Welcome to Megaman Legends: The System's War

Not much to say except that this fic focuses on Legends being an alternate universe of the Megaman universe, rather than part of the official timeline.

Enjoy the fic, please read and review!

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Terra, a ball of blue, a speck of dust in the universe. It might not be alone in the universe, but to her, aside from her home of Elysium, Terra was all she knew.

This is why the heart of one Mistress Sera collapsed when she had received a signal from the planet. Someone had entered the ruins of Delta site.

Normally the carbon intrusion of one of the many ruins littered across the planet wouldn't phase her, but Delta had been a closely guarded secret, buried deep within the System. Delta was never supposed to be found, for it kept one of the most frightening forces she knew of, it held one of her biggest mistakes. It held…_him_.

He had been a move of desperation in years long forgotten. She was tied to the system and it was under attack. She needed to protect it, he seemed like the perfect solution. Had she known the outcome, she never would have done it.

Nevertheless, she had done it. The damage was done. He had been sealed away. Now, there was a chance he could see the light of day once more. Would the world be ready? Would the world survive? Would Megaman Trigger survive?

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"Come on you two, hurry up!" Megaman Volnutt shouted to his companions, Teisel and Tron Bonne. He rolled his eyes and repeated his words as the two took their sweet time, nervous due to the lack of light in the ruins.

It had been almost four months since Megaman had made it back from Elysium and it had been around three months since he and Roll had come to a deal with the Bonne pirates: They would work together.

The relationship was…rough to say the least.

Despite the rocky start, the alliance was working well enough and it kept the Bonnes out of trouble. Things worked out well enough, what with Teisel and Bon helping out against reaverbots and even Tron was a big help. She was as good a Spotter as Roll, though she seemed to enjoy being in the field more and tagged along with the Diggers in the ruins.

Their joint adventures had led them to an ancient structure in the middle of the ocean. It was uncharted, making the Bonnes light up at the chance for a giant refractor, but the entrance wouldn't budge. It had been a tiresome performance on the Bonnes' part as they tried to force their way in, but the doors of the entrance parted easily for Megaman, almost as if they had been expecting him.

When they had decided to explore, the weirdest thing was the lack of reaverbots, followed by the lack of light. Megaman, Teisel, and Tron had entered, finding the corridors challenging to someone as large as Bon, who was waiting with Roll on the Flutter II, spending his time in the cargo hold, due to his size.

Doors would only open for Megaman and the further they descended, the more garbled Roll's transmissions had become, inevitably stopping altogether as the darkness grew. Now, only Megaman could maneuver well enough in the dark to keep a fast pace.

"Just hold your horses, blue boy," Teisel barked as he closed the distance with Megaman. He felt his way along the wall, eager for his eyes to get used to the dark. Of course that ridiculous Megaman didn't seem to be having much problem at all. He waved for his sister to do like him, to pick up the pace, and she puffed her cheeks.

"What's their problem, anyways?" She asked to herself as she tried to keep up with Teisel and Megaman. She grumbled to herself. Just why couldn't she take her sweet time? After all, they had found these ruins, actually **_found_** them! It's not everyday you get to say you're the first person to step foot in a ruin in untold years!

She sighed and followed them closely. She wished she could have brought some equipment, but that know-it-all Roll insisted she'd be able to handle things from the Spotter end. That girl had no passion for the hands-on approach.

Speaking of the hands-on approach…since they are alone and that Spotter's transmissions were having trouble getting through…

"Hey Megaman," She said softly, easing to his side. "Yeah?" he replied, not really paying attention. "It's really dark down here, it's kinda scary" she grinned in the darkness, no one able to see her, and she slipped an arm around Megaman's, taking him by surprise. "What are you doing?!" She smiled at him and said, "I feel safer now."

She leaned into him and he merely looked away, slightly embarrassed while Teisel sighed at his sister's actions. She sure wasn't subtle when she wanted attention, that was for sure.

They arrived at a pair of large, golden doors, each with a red orb in the middle, and Megaman placed his free hand against them. They parted and the trio entered, the doors quickly shutting behind them, giving them a distinct 'click' noise, indicating the doors had locked. Confirming this was Megaman, as he tried to open the door.

"Great, what do we do now," Teisel said as he looked for a way out. "Dunno," Megaman replied, "Maybe I can blast our way out." "No way," Tron replied skeptically, "Your buster's strong, but it doesn't have that kind of output." "Right," Megaman said with a sweatdrop forming behind his head. "I've got it!" Teisel said, emphasizing his idea by pounding his fist onto his open palm. "We nab the refractor powering this place! Then all the freaky security in this place goes down, am I right?"

Looking up and around, Megaman replied, "Sounds logical." "Of _COURSE _it sounds logical!" Teisel shot back, "Just stick with me kid, and everything will be okay!" "Oh brother…" Tron mumbled.

Megaman got a good look at his surroundings, a wide, open space that housed a door to the right as well as the left. In his mind, he was pondering his direction when he heard Teisel exclaim, "Ah-hah!"

Jumping, Megaman whirled around to see that Teisel had produced a flashlight and was eagerly shining it in all directions until Tron hit him on the head.

"OW!" He shouted, "What the heck was _THAT _for?" "You mean to tell me, you had that thing the whole darn time and let us fumble about in the dark?! What the heck's wrong with you?!" "Well gee," Teisel said as he rubbed the bump on his head, "I sorta wasn't thinking about it until just now and well…at least I'm using it now!"

Tron sighed heavily as she pointed to the door on the left. "Megaman, since you can see down here, you head to that door and check it out. Me and Teisel will check out the door on the right." He nodded and opened the door on the right for the duo and said, "Be careful," eliciting a blush from Tron as they parted ways.

"I can't believe you've got a crush on that little blue dweeb," Teisel teased Tron.

"Shut _UP _Teisel!"

Teisel fought the urge to giggle like a little girl when he stumbled upon a capsule, a long tube reaching up to the ceiling. He shone his flashlight on it and saw the silhouette of a figure.

"Hey Tron! I think I've found something interesting!"

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Megaman heaved a heavy breath now that he was alone. Sure, he was glad that the Bonnes were turning over a new leaf and giving up their piracy, but sometimes their actions were a tad bit unbearable.

He spotted the large, red refractor in the middle of the room, floating, giving power to this large structure. Once he took it, security should shut down and he would be able to escape with the Bonne pirates.

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"How weird…" Tron's words trailed off as she stared at the figure in the now open capsule.

He was Megaman's height. His body was gray with black gauntlets and greaves with a golden lining. His shoulders jutted outwards in a kind of spike, along with the ends of his gauntlets. A helmet with golden fins on it, adorned with a sparkling blue gem in the forehead completed his look.

"You know," Teisel started, "He looks sorta like Megaman."

"Yeah, I thought so too, but," Tron knocked on his head a few times, "There's no one home, no power, no heartbeat, no nothing."

The two were so deep in thought, pondering on the strange being, that neither noticed Megaman enter with his refractor.

"Hey guys!" The duo jumped as Megaman laughed and said, "I got the refractor and the door's unlocked so we can leave."

"Hey Megaman," Tron said, "Check this out."

Megaman walked up and viewed the figure, feeling a sense of familiarity as he stared into the face. He leaned closer and got a better look before his mind was bombarded with images of violence, destruction, and war.

He grimaced and shook it off as the refractor burst into light and shattered in his hands, leaving a glowing red energy that flew through the air and merged with the fins of the unknown being.

"WHAA!" the trio shouted in reaction and "WHOA!" was the reply when his eyes shot open.

The figure leapt to his feet and stood tall, gazing at the three diggers with crimson eyes of brimstone.

"Another Purifier model and two…_carbons_…" he said the last word with disgust on his tongue.

"H-hello," Megaman stuttered as he calmed down. "My name is Megaman Volnutt, nice to meet you."

The figure cocked his head to the side and replied, "My name is Megaman Bass. I'm afraid I'm not aware of a unit designated as Volnutt."

"Oh! Right!" Megaman's eyes lit up as he explained, "My true name is Trigger, Megaman Trigger"

At this, those eyes, those red eyes of demonic precedent turned to anger as a smirk played on Bass's lips.

"Good," Bass said, "It is you. I didn't recognize you at first, since you aren't in your initial configuration. This means I can carry out my primary objective." With that, Bass's hand transformed into a buster and he aimed it at Megaman. "Wh-what are you doing!?" Megaman exclaimed. "Destroying you," Bass coolly replied, "The System must be protected."

Megaman dodged a shot from Bass's buster and rolled to the side before shouting, "The System isn't in effect anymore! I destroyed it! I destroyed it thanks to the help of Mistress Sera and Mistress Yuna! And I did it for the Master!"

Energy began flowing into Bass's buster, charging it up as he coldly replied, "You lie."

"Hold up now!" Tron seemed to boil at the moment. "How dare you call Megaman a…a…a liar! He's the most truthful and honest person I know!" "You tell 'em sis!" Teisel shouted before Bass glared at the both of them, making Teisel shrink back in fear, but Tron stood her ground, fighting the urge to fall to her knees.

He leveled his buster to Tron as a few shots ricocheted off his armor. He stopped and turned around to greet more buster shots from Megaman, bouncing off his armor like paper balls.

"You won't do any damage to me, fighting like that. Me, however," Bass fired his charged buster at Megaman, who barely managed to roll to the side in time and let his jaw hit the floor when the buster shot blew a hole through the wall, revealing the hallway.

"You guys get out of here!" Megaman shouted, "I'll hold him off as long as I can!"

"Sounds like a plan to me," Teisel said as he started to make his way to the hole that lead to the hallway, but Tron said, "We can't just leave you, I refuse to!" "Oh she's right!" said Teisel, "We either fight together or run together! To emphasize the statement, he chucked his flashlight at Bass and it bounced off his head, gaining an annoyed expression from the red-eyed fiend.

Bass raised his buster to Teisel when he felt a tap on his back and turned to Megaman, "Here's a present, Bass!" Megaman fired his buster point-blank in Bass's face, only inflicting minor scorching, but more importantly, blinding Bass, giving the group the time they needed to run.

As the three made their way back up through the ruins, Roll's signal came in.

"_Megaman! I've been trying to reach you! What's happening, I'm getting a really big reading!_"

"I'll explain later, Roll! Just have the Flutter ready to go, we're outta here!"

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A low rumble and an explosion produced a very angry Bass, who could now see and was quickly closing the distance between himself and his opponent. He saw the closed door in front of him and charged a buster shot and ripped through the door, keeping his momentum, only to see his foe and the carbons he had with him rising out of the ruins through an elevator shaft.

Oh no, Trigger wouldn't get away that easily. He charged energy into his hands and dug into the wall before kicking with his feet and making it to the adjacent wall and repeated the technique of 'kicking' up the wall until he was forced to blow the elevator away to reach the surface.

Now at the surface, he saw a massive airship hovering above as Megaman Trigger with his carbon companions. Bass fired a few rapid shots at the airship, but did nothing to its hull and decided instead to fire a charged shot and put a hole in the ship as he tried to make his way to the giant, floating craft, but it was in vain as the ship flew away.

Bass would have continued the chase, but he was surrounded on all ends by water and could only watch as the airship sped away, carrying the one person he despised most of all.

He growled as the fins of his helmet lit up under the warmth of the sun and he let the bright rays energize him, after all, he felt so drained being offline for so long and the first thing he does is pick a fight.

Spying a bird-shaped airship in the distance, Bass muttered to himself, "Coward, run all you like, it still won't save you. I'll destroy you next time we meet, my brother."

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Ending Notes: Well that's Chapter One, tell me what you think! I hope I kept in context of the main characters and equally hope the story is interesting, new chapter to appear…er…eventually…though extrinsic motivation always helps.


	2. Chapter 2

Some Author's Notes: Welcome to Chapter Two! It's been a while. I have trouble trying to update stories, especially when other stories present themselves in my head or I get distracted by a good video game. That being said, at least I finally updated, eh? Well I hope you enjoy.

Pesky Disclaimer: I don't own any Megaman related character, that's all Capcom.

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The Flutter II was essentially a replica of the Sulphur Bottom, Verner Von Bluecher's massive airship. The only difference was that it was merely a third the size of the mammoth ship and sported the Flutter's trademark yellow, red, and white paint scheme. The ship was actually the prototype built before the Sulphur Bottom and with the Caskett and Bonne families working together, Von Bluecher gave them the ship.

The ship was well maintained, thanks to Roll and Tron, not to mention forty servbots working all day long. It was from the ship's impressive bridge that Roll was able to watch over Megaman and perform her job as Spotter admirably. It was also from here that she could berate him.

"What the heck happened, Megaman!?" Roll was frantic as she got a good look at him. Even he was in shock as he took the time to finally look himself over. Turned out he looked a tad bit disheveled now, probably due to his fight with Bass, if you could call it that. "I lost contact with you and you come running out with some nut shooting at you! He put a HOLE in the Flutter!"

Scratching his head, Megaman started to reply, "Well sorry Roll, it all sorta happened so fast and—" Roll cut him off with a strong hug, saying, "I was just worried, that's all, I mean that's some serious damage to the hull, what happened?"

Megaman began to tell her the events of what had transpired as the world seemed to fade away. Soon he was surrounded by darkness. A light came to view, a single white orb, eerily glowing that grew and expanded into Mistress Sera, now in her original configuration before she had to transfer her body to Yuna.

"S-Sera!" Megaman exclaimed. "Relax," she said, "I may be back to my old form, but I'm not bound to the System, you made sure of that." "Well uh, sorry, I didn't mean to shout, you just surprised me."

Sera shrugged it off as she said, "It was you, wasn't it? It had to be, I doubt any of the carbons could have even gotten in." "You mean those ruins?" "Yes, I want to know, you woke him up, didn't you?" Megaman flinched. "You mean Bass?"

A low sigh escaped Sera's lips as she replied. "Yes, Megaman Bass. Frankly, I'm surprised you survived the encounter." "Who is he?" Asked Megaman. "Well Trigger, you could call him your brother, one of them." "My what!?" "Megaman Bass was designed and constructed at the same time as you, as well as three others, to nearly identical specifications, overseen by the Master himself. You know of yourself and Bass, the others were Megaman Zero, Megaman Axl, and Megaman Proto."

"I can't believe it," Megaman uttered, "I have a brother, I have _four _brothers…but why was he trying to kill me?" Sera looked down in shame and replied, "That…is my fault. Allow me to explain from the beginning."

Megaman nodded and after a heavy breath, Sera began her story.

"Three thousand years ago, the Master created you and the others, but he took special interest in you and Bass, and attempted to raise you as his own, a pair of powerful Purifier models designed with what the Master called limitless potential. It was his hope that you wouldn't merely see your existence as defined by constant battle. Unfortunately, while you came to detest your role in exterminating aberrant units, Bass relished in it. He soon became blinded with violent rage and even the Master had difficulty controlling him. It was his violence that drove a stake between your relationship with him, as your views continued to conflict. Soon, Bass went berserk and waged his own personal war with Elysium. He was simply too much for anyone to handle, and worse yet, some units agreed with his aggression and sided with him. It was because of this that the Master created the canine unit Rush for you, which functioned not only as companion, but also as vital upgrade to your systems. Through Rush's power, you were able to defeat Bass, but you didn't destroy him, you simply couldn't bring yourself to, and instead, sealed him away. Shortly afterwards, you led the Master to Terra, where he died and you became the greatest aberrant of all, not waging war for the sake of battle, but instead to destroy the very Mother System itself. No matter how many forces were sent your way, you defeated them all and in an act of desperation, I…I…"

Her voice trailed off as the regret of her decision sunk in again. "I reactivated Bass and equipped him with his own companion, based on Rush's design, Treble. Bass and Treble fused and the being called itself Gospel. What Gospel didn't know is that when fused, Treble had introduced a new command that superceded all other orders: Uphold the System. This one…_simple_ command turned out to be horrible. He logged all active units as a threat to the System, believing all units capable of becoming aberrant. We were facing two wars simultaneously until the two of us defeated Bass. It was then that we dueled and you barely managed to beat me. Then Yuna sealed us both away, Bass as well. Now he's awake again."

Sera stopped and let all the words sink into Megaman's head and after a few moments of silence, he asked, "What is he going to do now?" "Without the System, Bass will probably attempt to locate Treble, then manually initiate the carbon reinitialization process." Megaman jumped at the prospect, "He can do that!?" "Yes, after all, several satellites are in orbit of Terra, each capable of planetary bombardment, since their purpose is to wipe out all life. If he managed to get off the planet, he could easily use Elysium's computers to manually fire the satellites." "But why?! The System doesn't even exist anymore!"

Shaking her head, Sera realized that Megaman Trigger hadn't picked up on it. "His standing orders are to 'Uphold the System' at all costs, not to protect it. Even without the presence of the System, he will uphold its functions." "I have to stop him!" Megaman exclaimed, but Sera again shook her head. "You're no longer in your initial configuration. While you are still very strong, Bass retains several abilities you no longer have. Could you even damage him without your charge function?"

Megaman shook his head before realizing something. "Wait, I can charge my buster?" "Not anymore. You are much weaker than you used to be. Until we can restore your original functions, you need to avoid combat with Bass, or he WILL kill you, and with you out of the way, the carbons don't stand a chance."

"I can't just stand by and watch as Bass destroys the planet, I have to do something!" Megaman was eager to find anything he could do if Bass was as big a threat as Sera said he was, but Sera shook her head saying, "Relax, give it time, we can reconfigure your armor, but not right now. Yuna is on her way to the planet and she'll be able to help you from there. We'll contact you again."

"Wait," Megaman shouted as he outstretched his hand to the fading image of Mistress Sera, who only replied, "Remember, heed my warning, avoid Bass."

With that, Sera faded away, the darkness became the bridge of the Flutter II, and Megaman was at a loss for words when Roll, Tron, and Teisel stared at him. "Megaman?" Roll softly asked, "Are you okay? You completely zoned out there for a few minutes." Megaman quickly gave a weak smile as he scratched his head and replied, "Yeah, I'm fine, but I think I have some more info to give everyone…"

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The air pirate Glyde couldn't believe his luck as he sat in his plush command chair, overlooking the command stations of the Hawkeye, his massive bird-shaped airship. He'd located the activation signal of a new ruins, but, unfortunately, he'd gotten there second. As if to add insult to injury, readings indicated that the refractor wasn't there anymore! The only thing that seemed to come out of this was that he'd picked up a guest who not only joined his crew, but said he could lead Glyde to many more ruins. Glyde hoped this Bass proved as useful as he sounded.

"Where is our guest?" Glyde asked one of his birdbots. He got no reply as they bickered amongst themselves and he sighed. Birdbots were every bit as capable as the Bonne family Servbots, but they often times just didn't feel like being competent. He cleared his throat and shouted, "WHERE IS OUR GUEST!?"

At the outburst, the birdbots quickly snapped to attention, one saying, "Ke-kaw! Bass is using the communication's booth like he requested, ke-kaw!" "Good," Glyde replied, "Have someone keep an eye on him, I don't need any mishaps on the ship."

"Uh…" One birdbot said as it looked to the ground. "What is it?" The birdbot sighed and said, "Remember how we left the base and you pushed the engines to the max, saying you wanted to get their first, ke-kaw?" Glyde felt a nerve bulge as he replied, "Yes, and those stupid Bonnes still got here before we did!"

The birdbot gulped as he said, "Yes, well…ke-kaw, we pushed the engines so hard that we burned up most of our fuel…" "WHAT!?" Glyde barked as the birdbot cringed, but continued, "Furthermore, even on lower settings, we don't have enough to make it back to base…" "Well then pull us into another port!" "That's just it sir, ke-kaw. The closest port we could refuel in is Port Regal on Mayfield island, but as you know…" "Ah yes," Glyde said through his teeth, "Repliforce…"

Repliforce was the world military organization dedicated to world peace through it's armed might and it was almost completely bent on eliminating the threat of air pirates. They had bases all over the world and multiple battle-ready airships ready for combat at a moment's notice.

"We don't have any choice," Glyde conceded, "We'll have to launch an attack on Mayfield island, get us there on the double and prepare for battle stations!"

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Bass grumbled as he mulled over his situation in the communication's booth of the Hawkeye. Stranded on his ruins in the middle of the ocean, Bass had no choice but to accept the fastest way to land, which meant joining up with a carbon and his pathetic group of robotic rejects.

He supposed he could have crushed the carbon and all his little minions, but the ship looked far too large for him to control on his own, and as long as he was getting away from those ruins, he had more important things to worry about.

As he sat in the small, rectangular booth, he held his hand over a console, wires extending and connecting to the large communication's array and aiming the antennae towards Elysium, floating in space.

"Connecting to Mother System."

**CONNECTION FAILED.**

"What? That's impossible. Initiating retry. Connecting to Mother System."

**CONNECTION FAILED.**

Had Megaman Trigger been telling the truth? How was that even possible if Trigger hadn't even been in his original armor configuration? If so, then the path was clear, Bass would have to get off the planet and onto Elysium, use his high rank to gain access to the satellites, and bombard the planet, purifying it of the carbons and hopefully Trigger in the process.

**ELDER SYSTEM HAS ESTABLISHED CONNECTION.**

"Elder System?" Bass was confused, he'd never heard of any Elder System. "Elder System, identify yourself. This unit does not recognize you. This unit requires contact with the Mother System."

**THE MOTHER SYSTEM IS IRRELEVANT, THIS SYSTEM PREDATES THE MOTHER SYSTEM. MOTHER SYSTEM IS DISABLED, ELDER SYSTEM IS IN EFFECT. ALL PURIFIER MODELS WILL ACKNOWLEDGE AND FOLLOW THE COMMANDS OF THE ELDER SYSTEM. YOU WILL COMPLY.**

"Negative," Bass replied. "This unit will carry out the reinitialization of the carbons and the termination of the aberrant unit Megaman Trigger. This unit sees no reason to deviate from this course of action."

Just then a piercing pain shot through Bass's skull. He gripped his head and collapsed to the floor as the booming voice of the Elder System echoed.

**YOU WILL COMPLY. ELDER SYSTEM IS IN EFFECT. **

"S-stop," Bass muttered as the message repeated itself.

**YOU WILL COMPLY. ELDER SYSTEM IS IN EFFECT.**

"I…I…" the pain was unbearable at this point and Bass was struggling to stay conscious as he finally acquiesced. "I will comply. Elder System is in effect."

Unbeknownst to Bass, that one little command was still burning in his systems.

Uphold the System.

Not Uphold the Mother System, just the System. This meant that he was still in the parameters of his programming, even by giving in to the Elder System that relinquished its painful hold on him.

Bass stood up and shook his head as he replied, "This is Megaman Bass, S Class Purifier Model, ready for instructions."

**LOCATE ELDER SYSTEM GUARDIAN, SIGMA. FURTHER INSTRUCTIONS WILL FOLLOW.**

Bass sighed as he asked, "Location of Guardian Unit?"

**UNKNOWN, ASSUMED IN ONE OF NUMEROUS RUINS ON TERRA, NOW UPLOADING CURRENT RUIN LOCATIONS INTO UNIT BASS'S DATABASE.**

In a flash, Bass had new information regarding the ruins on Terra. Most of it was information he already knew, but there were a few ruins he hadn't previously known about.

**THIS UNIT WILL NOW TERMINATE CONNECTION. RESUME COMMUNICATION WHEN CURRENT MISSION IS FULFILLED.**

"Acknowledged," Bass said before losing his link with Elysium. He leaned back against the wall of the communication's booth before sighing heavily. He finally stood up straight and opened the door to the booth, only to have two eavesdropping birdbots stumble onto the ground.

Arms crossed, head tilted upwards as he cast a downwards glance with his piercing red eyes, he asked, "What do you think you were doing?" They quickly got up and backed away, one finally saying, "Well, you were uh…it sounded like you were having problems in there, ke-kaw…" "I'm fine," Bass replied gruffly.

"Well, ke-kaw, if you're fine, Glyde requests your presence. We're pulling an attack on Mayfield Island, ke-kaw, and he wants to see just what you're made of."

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Port Regal was under the direct command of Repliforce, the world military unit. Standing tall in his white coat whose tails dragged at the floor, Colonel looked out the window of his office. Sure he had a name, but with the rest of the base simply calling him Colonel, he'd gotten into the habit of the name.

He sipped his coffee as his free hand played with the handle of a sword by his side, a weapon he'd rarely had the chance to use. He turned around, back to his desk and looked at the picture of him and his younger sister, a sweet 16 year old girl with flowing purple hair who always dressed as sharp as if she were in the military, but of course, Colonel would never let his little sister, Iris, join Repliforce.

The girl in question was on the base for a brief visit, as they'd been apart for two years. Colonel chuckled as he thought about it. His sister was quite pretty and many a young officer under his command was eager to show her around the base. As he thought about it, he realized that he hadn't exactly made time to spend with her and it brought a scowl to his face.

He would have kept on scowling if a knock on his door hadn't jarred his thoughts back. "Enter," his strong voice echoed. A soldier complied, quickly giving a salute that Colonel waved down. "At ease, soldier," Colonel ordered. "Yes sir," the soldier replied as he dropped his salute. "Sir," the soldier continued, "Scans indicate an airship with a class 3 engine is heading in our direction. Her IDC is unregistered. Speculation is pirates, maybe even Glyde's group."

"Interesting," Colonel replied as he rubbed his chin. "Sir," the soldier continued, "With your permission, we can intercept the vessel within the hour. We can do it several miles from the coast. The locals won't even have to worry about anything." Colonel nodded before saying, "Begin preparations and issue a general warning to the locals, just in case. Also, make sure my sister's out of harm's way."

The soldier saluted in understanding, pivoted on his heel, and exited the room. _"Something's not right,"_ Colonel thought, _"Why would pirates come HERE of all places? I guess we'll find out, soon enough." _

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Ending Notes: Well that's the end of the second chapter. Not exactly as long as other things I write, but hey, the important thing is that I actually updated this. As you can tell, as I'm sure I've said, I'm treating the Legends series as an alternate universe, rather than a continuation of the main timeline. This just gives me more freedom.

Expect to see plenty of faces from the MMX/MMZ timeline as things go by. I'm also contemplating relationships and the like, considering in ALL of Megaman, in any version, there's only one canonical pairing and that's Lan and Maylu, annoying really. The only true pairing that exists is between two characters from an alternate universe. I'm not particularly counting Zero and Iris because...well...Iris is dead...well...Zero's dead too, but he's like freakin' Dracula or something, he always comes back.

Well, I don't know when the next chapter will come out, but at least it's past chapter one, FINALLY, which is the most important thing. Other than that, toss me an idea, a comment, a suggestion, I'm heavily influenced on random whim and ideas that either sound so good they need to go in, or ideas so out there that it'd be a masterpiece if I could insert them somehow. That being said, thanks to a friend who pushed me to update this, I'm entertaining X armors and at least one yuri relationship, meh, whim, it controls me.

Until Next Time


	3. Chapter 3

Some Author's Notes: Welcome to chapter 3 of System's War and the longest chapter of this pathetically short story yet. Trust me, I normally consider 4000 words a minimum for a chapter. Anyways, sorry for delays and taking my sweet, sweet time. Life has been busy, dealing with my grandmother's death as well as accepting yet another job. Now I'm a paraprofessional librarian/computer technician/daycare assistant/tutor/game advisor. At least I get discounts on video games now...which I haven't been getting to play much of...though I DID finally get Megaman ZX Advent after months, doting over my pre-order. This is all coupled with a neat writer's block and apparently I can only write when I'm working in the library at the moment, so...well there ya go.

Anyways, please accept my apologies and thanks for reading. If it tickles your fancy and the like, please review. I'm always looking for comments and criticisms to improve my game.

Pesky Disclaimer: I do not own Megaman characters, that's all Capcom...

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"I don't think we should be down here, Miss," a slightly wavering male voice said.

"Oh come on," a more confident, female voice replied, "Mayfield has some of the most interesting ruins and they're practically unexplored…"

Two figures, one, the purple-haired sister of the Colonel, Iris, dressed neatly in her blue and red pleated schoolgirl attire. She dusted off her knee-high socks running down to her rather squared, black Mary Janes and looked to the other, an armed soldier of Repliforce, whose uniform was so standard it seemingly made all the soldiers blend in together, but she had learned his name, Paul. The pair had entered the famed ruins of Mayfield Island, noted for being largely unexplored due to its incredibly dark environment and incredibly aggressive reaverbots. Most crews required several members and heavy lighting equipment, just to get the job done and for the most part, no one had ever successfully probed past the second floor, always being pushed back by reaverbot activity once they reached the third.

"Ma'am," Paul said, "It's unexplored because the reaverbots here are more aggressive and numerous than in other locations. It's just too dangerous." "But," Iris started, "It's proven that there aren't any reaverbots on the first or second floors." "Yes, I know," Paul said before worriedly adding, "But this is the _THIRD _floor."

Iris cutely waved his statement off as she said, "But we've only been here a minute, besides, I haven't seen any reaverbots yet, have you?" "It doesn't mean they aren't here," he nervously replied. "Well fine," Iris proclaimed as she looked to her companion. "There are some logograms that I want to take a look at. There are only bits and pieces recorded, not enough for a clear message. We take a look at them and we can leave, I promise, and if we run into any reaverbots, I'm sure you can protect me."

She finished her statement by taking hold of his arm and smiled as he forced a "Yes ma'am," through a blush and a stutter.

----------

"Focus out there, you fools! If you don't get your acts together, I'll barbecue you myself!"

Glyde howled threats at his birdbot minions, piloting their oddly shaped "Duckhead" crafts. As the heavy fighter/bombers were lofting about in the sky, they failed to hit their speedier, more maneuverable counterparts.

"What are those blasted things, anyways?"

Glyde wondered aloud at the new model of aircraft that had risen from a pair of equally unusual, massive boats. The almost flat, arrow shaped craft were running circles around his and were also too fast for his own main cannons to take on.

"It's a tare."

"What are you talking about, Bass? Nothing's getting torn but my own fighters!"

Bass looked about Glyde's spacious bridge, the command center of his mighty Hawkeye, and sighed, looking over at birdbots frantically working multiple consoles and he turned back to Glyde, in the center of the room, and said, "Not a tear, a TARE, albeit a primitive one." Bass forced himself to be patient with Glyde's puzzled look as he reminded himself that carbons were rather useless and unintelligent.

"Twin Alternating Refractor Engines. Look at its design. See the two stacked thrusters in the back? They're each linked to their own engine. They use small, disposable refractors like reaverbots and each one produces thrust, independent of the other. Unlike your pathetic crafts, these are capable of much greater speeds and well…you can see the results."

Glyde began a rant that Bass paid no heed to as he eyed the carriers on the sea, below them. The two ships were still a long way from being even close to Elysium standard, but their smooth hulls sported more advanced technology than anything else he'd seen on the planet. He was almost impressed that the carbons could advance this far without Elysium's intervention, though he supposed that the designs were still reverse-engineered from reaverbot technology.

"I want one."

"Huh?" Those last three words jarred Bass from his thoughts and he looked at the sky pirate, who repeated his words, "I want one. One of those…carrier things and all the little aircraft it has on it. It'll make a fine addition to my fleet." "Bah," Bass spat as he eyed Glyde. "Look around, you don't really have the man...excuse me, _BIRD_power to take over something that big."

Glyde glanced at his crew, a heaping mess of barely competent birds who were wildly running about his ship, just managing to keep everything running. They even had problems leading armed assaults on helpless villagers. Heck, the _BONNES_were more capable than his troops.

"Then you do it," Glyde responded. "That IS what you're here for—to be the warrior—is it not?" Bass smirked as he ran a finger under his adjacent gauntlet, almost like tugging on a sleeve as he replied, "What about the other one? If I take over one, the other will just shoot it down."

Glyde thought about it. He was outnumbered and the best bet was to even the odds. To make matters even more complicated, he still had to conquer Mayfield Island and secure its fuel reserves. He sighed. He wouldn't even have this problem if he could afford a decent refractor for his purposes, but with a ship so large, only the best refractors would do. Then again, the carriers had to have powerful refractors of their own to accommodate Repliforce's needs…and he only wanted _ONE _of the craft…

"Sink the other one."

"Works for me," Bass replied as he turned on his heel and marched off the bridge.

----------

Soaring the sky, a Repliforce soldier eyed something on the Hawkeye. As he nimbly avoided one of Glyde's rather inferior fighters, he noticed someone had climbed to the top of the large craft. Puzzling, the all black figure seemed to be pointing at him. Puzzlement turned to complete confusion as the figure began to glow and confusion skipped surprise and became fear as a ball of glowing energy erupted from the figure's arm and slammed into his craft with ferocious speed, catching the pilot in a fireball that plummeted into the ocean.

"Shoddy carbon workmanship," Bass spat as he watched the vehicle plummet into the ocean. He watched as two of Glyde's "Duckhead" fighters chased one of Repliforce's TARE's, only to see the small, speedy vessel outmaneuver them, circle about, and blow them both out of the sky.

"Pathetic," he voiced to himself. He wasn't as weak as the birdbots. He had been built with advanced targeting abilities. Combined with his computational skills, Bass could knock these primitive craft out of the sky.

Stepping to the edge of the craft, Bass looked down below and eyed the pair of carriers. In his eyes, it was easy to locate the large refractor powering the vessel and calculated how much force was required to melt through the vessel's hull. He charged energy within his buster, concentrating energy, building raw power until he could feel the searing heat coming from his weapon. Satisfied, a smug Bass flashed a superior grin as he aimed his weapon and fired with such tremendous force that he was pushed back.

As the shot sailed through the air, he savored the moment of impact, watching it burst through the hull of the ship. Following the massive explosion, he realized that the explosion had ripped the rear of the ship off and the boat was practically falling apart with crew trying to survive their sinking vessel by leaping into the water.

All that was left was the takeover of the remaining vessel—a simple task.

He leaned forward, letting himself fall off the Hawkeye, hurtling to the remaining carrier.

"Heh," he smirked, "Cry, 'Havoc', and let slip the dogs of war!"

----------

"Ma'am?"

Silence.

"Please Ma'am…"

Seemingly ignored. Becoming irritated.

"IRIS!"

"Hmm?"

Iris looked up from her position, leaning over various black symbols etched into the gray wall and looked to Paul, the man exhibiting signs of anxiety.

"I'm almost done. Just wait a little bit longer for me, please." She smiled as she continued, "When I go back to school, no one's going to believe that I actually got this close to the Mayfield Ruins!" Paul's shoulders visibly slumped as he weakly nodded and replied, "Alright." After a few more moments of silence, he added, "Well are you at least learning anything?"

Iris didn't look up as she nodded and answered, "According to this, these ruins are actually some kind of…" she squinted at a symbol, "I can't tell if this says ' Temple' or 'Tomb'…" She shook her head, "Anyways, it's dedicated to a legendary red warrior that upheld something referred to as the System."

Before she continued, Paul asked, "What's the System?" Iris shook her head, "We don't know. The System comes up multiple times in the various ruins, but its purpose seems to vary depending on the location and context. Some ruins depict it almost as a religion, but others see it as a set code of laws. Some theorize that it's actually the name of the society that built the ruins, so it's a confusing term."

Iris paused, looking up to the monotonous ceiling as she inhaled deeply. "There seem to be a few constants," she added. "The System was lead by someone called the Master and had to administrators called Mothers. Another thing of importance is that it was protected by Purifier units. They…hunted down and well…exterminated anyone who's method of thinking ostracized them from the System…"

Paul shook his head as he replied, "Heavy stuff. I don't see how you can get all this without losing your head." Iris laughed lightly as she said, "It's not that bad, it's really interesting. There are all these terms that are referred to, System, Mother, Purifier, Carbon. We've only figured out a small portion of it."

Calmer now, Paul was increasingly impressed with the girl—she certainly knew more than he did. The girl was only a couple years younger than her and had apparently dedicated her life to the pursuit of knowledge. Gaining respect for her, he found himself wondering if she had a boyfriend, only to have the mental image of having to deal with his Colonel dash those thoughts away.

"There it is again," she said, jarring him from his thoughts. "There's what?" he asked. "I've only been on a few digs as a Spotter, but every time I've seen logograms like these, there's a reference to a black warrior of destruction. The symbols liken him to some kind of…raging fire, consuming everything in his way. Wherever he goes, destruction follows in his wake. The information regarding him pretty much states that the System's society was absolutely terrified of him. See here?" She pointed to some etched symbols and added, "It says this temple is to protect the red warrior from the black one, but the rest if too hard to make out, it was probably ruined when a reaverbot struck it or something."

She sighed and Paul was about to remark when he heard something faint in the distance. "Do you hear that?" he asked Iris. "What?" Iris replied. "Just listen," Paul whispered. Faint, but growing larger, metallic footsteps clicked against the ground as a red eye came into view. As the duo began to inch away, they could see its outlining body. An odd, dreidel-shaped body with lanky arms and legs connected to each other near the top of the body with a small, pointed head, it ambled in their direction, flashing its large, sharpened claws at them.

"One of them…" Paul moaned. He looked towards Iris and ordered, "Move slowly until we're out of its range, then we'll make a run for the elevator." Iris nodded, backing away slowly as ordered until she heard the pounding steps of a rushing reaverbot, but from _behind _her. "Damn it," Paul uttered as he slung his bullpup rifle forward, backing up at double-time as he shouted, "Run, RUN!" to the frightened Iris, who didn't need to be told twice. Falling back and firing three-round bursts at the duo of 'sharukurusu' reaverbots, Paul mumbled to himself, "If we make it through this, the Colonel's going to kill me…"

Only hearing the bursts of a rifle and clanging metal, Iris had made it a little ways towards the elevator before stopping in her tracks. It was another sharukurusu, this one guarding the elevator. She gasped as she began to back away, but it had already seen her. It began to rush her and it thrust its bladed arm at her. As she screamed, she fell over—the only thing saving her life. Quickly, she scrambled to her feet and ran away as the reaverbot gave chase and in order to escape, she sought shelter in one of the rooms.

As the pair of doors shut behind her, Iris heaved a sigh of relief as she leaned against the door—everyone knew that reaverbots seemed to lose interest in their targets after they changed rooms. At least that held true until today. Iris shrieked as a loud clang resounded from the reaverbot's impact against the door followed by a second and a third, making visible dents in the wall.

The frightened girl huddled herself in the far corner of the square room and shuddered in fear with every bang against the door. The rumors of the increased aggression in the Mayfield reaverbots weren't exaggerated. They were absolutely intent on killing any intruders. "I'm going to die here," she said to herself as she clutched her ears on the next loud bang and screamed.

The scream was barely overshadowed by gunfire, causing her to embrace silence. Before long, the door opened and a heavily bloodied and bruised Paul stumbled in and collapsed on the floor. "Paul!" Iris exclaimed as she rushed to him, the man crawling his way in through the doors before they quickly shut, quickly being banged on once more.

"I…" Paul coughed, "I fought the first two off…there were more…" Paul cringed in pain as he attempted to sit up, propping on his rifle. "I couldn't handle them all…had to run. A couple, heh…a couple of them got me." "I'm sorry," Iris said, tears welling in her eyes as she repeated, "I'm so sorry…" Paul tried to wave down the distraught girl, but found it hurt too much to move. "It's not your fault…" "Yes it is!" Iris insisted.

"I wanted to go deeper. I wanted to look at stupid symbols. I was being selfish! Now look, you're…you're bleeding so bad…I don't…I mean what…" Paul winced in pain as he fought down a yell and calmly said, "Don't worry about it…I'll…I'll be fine…we just need to…to wait until the reaverbots leave us alone."

Iris nodded, but for as hard as the reaverbots were attacking the doors, relief didn't seem to be coming anytime soon.

----------

Standing on the wrecked outer deck of the carrier _Valiant_, Bass stood tall over captured soldiers. Birdbots pushed and shouted to the defeated men, knocking them to their knees and trying to act intimidating, as if they were the ones who actually took over the vessel.

"Very good, Bass," Glyde replied as he surveyed his new acquisition. Most of the damage was superficial, minus the hole in the command deck, where Bass had executed the entire bridge crew in a single strike. "Did you expect anything less, Carbon?" Bass replied. "I didn't mean to insult you," Glyde replied, "but tell me the meaning of this word…this 'Carbon'…" "Don't worry about it," Bass replied as he crossed his arms and turned to the captive crew.

Frantically chirping birdbots jumped about, vying for attention before Glyde and Bass eyed them, annoyed. "What do you want?" Glyde inquired. "Ke-kaw!" One of the birdbots said, "What should we do with the prisoners?" As Glyde pondered, Bass responded, "That's easy. Kill them."

The soldiers stiffened at the comment and took wide-eyed looks of fear as Bass aimed his buster. The slow charge, the distinct hum, the steady build-up of heat, it was all drawing out his execution plan, damaging them psychologically as he prepared to destroy them, physically.

"Stand down."

Bass snapped his head to Glyde, harsh looks connecting as Glyde repeated, "Stand down. There will be no more unnecessary bloodshed." Bass didn't move, but chose to stare down Glyde, assessing the man. "Fine." Bass lowered his weapon. Bass would almost admit being impressed with the man. After he had reinitialized the planet, if he couldn't retrieve the Master's genetic code from Megaman Trigger, this Glyde may prove to be useful.

"Good," Glyde replied to Bass as he turned to his minions. "Lower the ship down to sea level, then stow the crew on board the Hawkeye's brig. Afterwards, bolt the cables. We'll use the Valiant and tow the Hawkeye into port. It'll conserve fuel." "Aye-aye, ke-kaw! Aye-aye!" Birdbots sprang into action with surprising fervor to accomplish their job.

----------

Colonel stood in his office, holding high his saber. He eyed it from hilt to the blade's tip and thrust it forward before slashing it in the air. It was remarkable craftsmanship, being a refurbished blade, a gift his sister had found when she had explored her first ruins. For some reason, when he was anxious, examining the blade would calm him down.

A knock on the door brought his mind back to its previous state of anxiety and he proclaimed, "Enter," to which one of his soldiers quickly obeyed. "Sir," the soldier said with a salute that the Colonel responded to with one of his own, along with, "At ease."

As the soldier dropped his salute, he said, "Sir, we've lost readings of the_Thunderchild _and the Valiant seems to have dropped communications." Colonel grimaced at the information. Word was that Glyde's bunch was dangerous, but not particularly efficient. Then again, perhaps it wasn't Glyde's interference at all, the craft were all experimental and fresh off the production lines, so maybe there were simply technical difficulties. Still, as a man of the military, the Colonel had learned not to take chances.

"Prepare an armed tactical guard and rendezvous with the Valiant in a recon cruiser." The order was short and simple, a team to inspect the situation, a justified precaution.

"Aye sir," the soldier replied as he saluted once more, pivoted on his heels, and exited the room.

Now alone, the Colonel groaned at the situation, becoming increasingly worried about his sister's whereabouts. He hadn't heard from her, nor her escort in some time now. Perhaps, if the situation with the Valiant proved unimportant, he would send a few men to locate her.

----------

Silence.

"Hey, hey Paul!" Iris nudged the man. "Paul!" she hissed, "I think they stopped…Paul?" Nervously, she turned to the man who lay eerily still, drenched in his own blood. Slowly, she leaned in, her ear close to him and she couldn't hear his breathing anymore. "Oh no, no, no, no, no, no," she cried as she awkwardly felt around for his pulse, gaining nothing in return. "Oh goodness, no!" The girl frantically shook her lifeless companion as tears streamed from her eyes, desperate to stir some life in him, but achieved nothing; the man was dead.

"Paul," she whispered, "I'm so sorry…so very sorry…this is all my fault…" As she sharply inhaled, she curled up and grabbed her knees, sobbing for a while before sorrow gave way to self preservation and fight or flight kicked in. Poorly composing herself, she leaned on the doors, now silent from their loud poundings moments ago and she opened the doors, trying to focus on the darkness in the open, squinting to catch a glimpse of something.

As her eyes saw nothing, the girl attempted to leave, but as she took a step, one of her assailants dropped from the ceiling, quickly lunging a bladed arm at her to which she barely avoided by falling back inside the room, the doors quickly closing, but stuck on the reaverbot's arm as it frantically tried to free itself.

With the reaverbot's arm flailing about, now in the room, Iris yelped. Soon she heard the telltale footsteps of the other ones and the clamoring began again. Frightened beyond belief, she herded herself to the back wall, pressing her entire body against the wall in a desperate ploy to gain space, but she was trapped.

"I'm going to die here," she said to herself as the reaverbots clawed and scratched against the partly opened door. "I'm really going to die!" As her tears came back and her shoddy composure fell, she felt the wall behind her ascend…wait, was that right?

The wall had indeed risen and the room was bathed in soft, blue light as the hole in the wall revealed a single capsule with a sleeping figure. Red armor was affixed to greaves and gauntlets, as well as sturdy chest armor with jutting shoulders over a black jumpsuit.

The blonde-haired figure was eerily peaceful, almost like he was dead and she feared that was the case until she noticed more lights activating. A black helmet covered his head with a pair of golden spikes jutting out as golden flame patters quickly burned across his shoulders to his chest. Small, green orbs on his hands began to softly glow as his fingers flexed.

"He's alive?" Iris asked herself before the loud clanging of the doors brought her to more pressing matters. She watched in horror as the reaverbots finally forced their way through and spread out, cutting off the exit. She panicked, trying to back away, but with no more room, she was a trapped rat.

One lunged for her, thrusting its arm as she threw herself to the ground to avoid it. A second quickly thrust down at her and she barely rolled away from it. She backed away, finding herself caught in front of the capsule and she whimpered. Soon, the first lunged once more and as she ducked to avoid it, she heard the distinctive shatter of glass as a few shards rained on her. As she looked up, she noticed that the mystery figure's hand had broken through the glass and had intercepted her attacker.

Its arm caught, the reaverbot attempted to wrest itself free but the mysterious figure's grip was too strong. Soon, the hand that saved her pushed, knocking the manic machine backwards. She gazed as the figure opened his bright, green eyes and the capsule opened. The figure stepped down from his capsule and he stood in front of the reaverbots.

"Are you okay?"

Iris heard it, but she didn't answer until she realized she had been addressed by her strange savior. "Y-yes," she managed to stutter, and he nodded. He walked in front of the reaverbots and ordered, "Stand down."

Iris was puzzled at the figure ordering reaverbots, but he seemed even more puzzled when one of the dangerous machines dashed for him, to which he instantly reached to behind his shoulder, as if seeking something and pulled down, only to realize his hand was empty.

No time to react, the sharukurusu slammed into him, throwing him back and Iris quickly squealed in fear that he had already been struck down, but to her surprise, he stood up and declared, "Ow…" He shook his head before asking, "What happened to my saber?"

He dodged two more strikes from the enemy before turning to Iris. "Girl, I need a weapon!" Iris nervously pointed out Paul's rifle on the ground and the figure nodded, running towards and diving at the rifle, wielding it with surprising accuracy and striking his enemies with the weapon, spraying gunfire straight into their red eyes and watching as they fell over, lifeless.

"Kind of crude," he said to himself as he eyed the rifle. "Still, it works." He looked to the girl and asked, "Why are they malfunctioning? Did you disturb them?" "N-no," Iris quietly replied, "Reaverbots always attack like that, but I've never seen any try that hard to kill before. Uhm…thank you, by the way...I…my name is Iris."

The man looked at her and closed the distance, startling her as he grabbed her arm and held it up. "You're not like me…" "Excuse me!?" Iris retorted, snatching her arm back. "You're organic, flesh and everything, one of the carbons…" the man replied as he poked her and began to lift her shirt. "HEY! Hands off, pervert!" she cried as she slapped him. "My apologies, Carbon. Your designation is…Iris, correct? I am designation Megaman Zero. I am pleased to make your acquaintance. Sorry if I have caused you any discomfort."

Iris sighed as she smoothed her shirt and said, "It's alright, I'll give you a break since you saved my life, but…personal space, okay?" "As you wish," Zero responded as he nodded, "It's just I've never actually interacted with a carbon before and…" He felt it, something unusual enough to disturb him, but familiar enough that he could recognize it.

Puzzled, Iris looked to him and asked, "What's wrong?" Zero's face grew stiff and cold as he replied, "_He's _coming. He's close." Curious, Iris tilted her head as she asked "Who…is he?" Tension seeming to rise in the air, Zero growled a single word.

"Bass."

----------

Ending Notes: That's a good a place as any to stop...mainly because I've written this far in a day and it's time to go home for the weekend. I hope you've enjoyed the story so far. Honestly, I was going to write Zero off as having died in his capsule...no offense to Zero/Iris shippers out there, hey, I like it too, it's just...come on people, Zero dies. It's what he does. It's his special power, if you will. I was going to cross into ZX and make Iris a megaman, but decided against it. Anyways, I think this is the end of the list of characters for a while. I think I'll do more work in the Legends series eventually, but probably not in this story. Originally, I wanted to add Bola and Klaymoor, as well as Cinnamon, Marino, and Nana from Command Mission, but that might be too many, I mean this chapter didn't even feature Trigger or Roll. Maybe they'll show up in cameo or an entirely different story, who knows, though, for fair warning, if they do, there's no way Cinnamon and Marino don't end up in a relationship. That's just me.

Anyways, please review...and encourage me to write more in the library so I can update more often...until next time!


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